What would you make of a supermarket that offered a tin of baked beans for 50p but charged you £5 to enter the shop when you wanted to buy it?

This is, in effect, what happens to investors who want to put their money into super-cheap "tracker" funds.

These funds aim simply to match the performance of the stock market as a whole, rather than attempting to beat it. This makes the funds very cheap to run because there is no need to pay fund managers and researchers to identify undervalued shares.

Instead, the fund simply buys every share in the stock market index that it aims to track. This simplicity allows the trackers to charge much less than you pay for a conventional stock-picking fund – perhaps 0.1pc a year as opposed to 1pc a year.

And such small-sounding differences in annual charges can make a huge difference to the amount of money that you eventually make from your investments if you are a long-term saver.

But it is very hard for investors to get the full benefit of the low charges on tracker funds because fund shops have started to add their own fees on top – and in many cases these charges dwarf the cost of the fund itself.

The problem has been highlighted by the outbreak of a price war between online fund shops this month.

Investors are discovering that, under a new system of pricing imposed by regulators, fund shops have to make an explicit charge for administering their fund holdings. Of the big fund supermarkets to have announced new pricing so far, Hargreaves Lansdown will charge 0.45pc to hold your funds, while Fidelity's charge is 0.35pc and AJ Bell Youinvest will levy a 0.2pc fee.

At the same time as announcing its new prices, Hargreaves said it would offer a FTSE 100 tracker fund from Legal & General on which the annual charge would be 0.06pc. This small percentage goes to L&G – but you will also have to pay the much larger 0.45pc to Hargreaves. So your total cost is not 0.06pc but 0.51pc a year.

Is there any way to hold trackers more cheaply and benefit from their very low charges?

Investors have several ways to do this. The most obvious is perhaps to switch to a cheaper fund shop – especially if you have a very large sum to invest, in which case companies such as Alliance Trust Savings and Interactive Investor, which levy flat fees rather than percentages, will be much cheaper.

For example, if you bought HSBC's FTSE 100 tracker, which has an annual charge of 0.17pc, via Charles Stanley Direct, the 0.25pc fee charged by the fund shop would take the total charge to 0.42pc a year. But Interactive Investor, whose flat rate annual fee of £80 includes eight trades, would cost you just 0.25pc a year on a £100,000 investment, said Justin Modray of Candid Financial Advice.

Another way is to switch to a different type of fund. Many trackers, such as those mentioned above, are either unit trusts or "open-ended investment companies", which are very similar. But trackers also exist as "exchange-traded funds" or ETFs, while there is also a single investment trust tracker on the market.

ETFs are shares, so they can be bought through any stockbroker and most fund shops. Youinvest, for example, does not charge to hold ETFs in an Isa, self-invested pension (Sipp) or dealing account, although all stockbrokers will levy a charge when you buy or sell.

Vanguard has a FTSE 100 ETF tracker with an annual management charge of 0.1pc, while dB x-trackers fund (dB represents Deutsche Bank) has a similar fund with a total annual cost, which includes additional charges, of 0.3pc. SPDR, whose British arm is run by Eleanor Hope-Bell, has a FTSE All Share tracker with the same charge.

Britain's only investment trust tracker, the Aberdeen UK Tracker Trust, also has a total annual fee of 0.3pc. Better still, the trust currently trades at a discount to the value of its assets of 3.8pc.

An ETF or investment trust bought via Hargreaves Lansdown still attracts a fee of 0.45pc but, crucially, it is capped at £200 a year.

Ms Hope-Bell said: "The total expense ratio of an ETF is the same for every investor, whether you have invested a small or large amount, whereas the total expense ratio for units in mutual funds can vary significantly depending on the size of your investment or the route you take to make your investment."